The Community and Phylogenetic Diversity of Biological Soil Crusts in the Colorado Plateau Studied by Molecular Fingerprinting and Intensive Cultivation
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Belnap, J, Gardner, JS (1993) Soil microstructure in soils of the Colorado Plateau: the role of the cyanobacterium Microcoleus vaginatus. Great Basin Nat 53: 40–47
Belnap, J, Lange, OL (Eds.) (2001) Biological Soil Crusts: Structure, Function, and Management, Vol. 150. Springer-Verlag, Berlin, Germany
Belnap, J (1994) Potential role of cryptobiotic soil crust in semiarid rangelands. In: Monsen, SB, Kitchen, SG (Eds.) Proceedings Ecology and Management of Annual Rangelands. USDA Forest Service. Intermountain Research Station, Ogden, UT, pp 179–185
Boyer, SL, Johansen, J, Flechtner, VR (2002) Phylogeny and genetic variance in terrestrial Microcoleus (Cyanophyceae) species on sequence analysis of the 16S rRNA gene and associated 16S–23S ITS region. J Phycol 38: 1222–1235
Bowker, MA, Reed, SC , Belnap, J, Phillips, SL (2002) Temporal variation in community composition, pigmentation, and F v/F m of desert cyanobacterial soil crusts. Microb Ecol 43: 13–25
Buckley, DH, Schmidt, TM (2003) Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5: 441–452
Don, RH, Cox, PT, Wainwright, B, Baker, K, Mattick, JS (1991) “Touchdown” PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19: 4008
Garcia-Pichel, F, Belnap, J (1996) Microenvironments and microscale productivity of cyanobacterial desert crusts. J Phycol 32: 774–782
Garcia-Pichel, F, Belnap, J (2001) Microenvironments of biological soil crusts. In: Belnap, J, Lange, OL (Eds.) Biological soil crusts: structure, function and management. Springer-Verlag, Heidelberg
Garcia-Pichel, F, Lopez-Cortez, A, Nubel, U (2001) Phylogenetic and morphological diversity of cyanobacteria in soil desert crusts from the Colorado Plateau. Appl Environ Microbiol 67: 1902–1910
Garcia-Pichel, F (2002) Desert environments: biological soil crusts. In: Bitton, G (Ed.) Encyclopedia of Environmental Microbiology. Wiley, New York
Garcia-Pichel, F, Johnson, SL, Youngkin, D, Belnap, J (2003) Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado plateau. Microbial Ecol 46: 312–321
Garcia-Pichel, F, Belnap, J, Neuer, S, Schanz, F (2003) Estimates of global cyanobacterial biomass and its distribution. Arch Hydrobiol/Algol Stud 109: 213–228
Hughes, KA, Lawley, B (2003) A novel Antarctic microbial endolithic community within gypsum crusts. Environ Microbiol 5: 555–565
Jackson, TJ, Ramaley, RF, Meinschein, WG (1973) Thermomicrobium, a new genus of extremely thermophilic bacteria. Int J Syst Bacteriol 23: 28–36
Jagannadham, MV, Chattopadhyay, MK, Shivaji, S (1996) The major carotenoid pigment of a psychrotrophic Micrococcus roseus strain: fluorescence properties of the pigment and its binding to membranes. Biochem Biophys Res Commun 220: 724–728
Johnson, SL, Charles, R, Budinoff, CR, Belnap, J, Garcia-Pichel, F (2005) Relevance of ammonium oxidation within biological soil crust communities. Environ Microbiol 7: 1–12
Joseph, SJ, Hugenholtz, P, Sangwan, P, Osborne, CA, Janssen, PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69: 7210–7215
Kishimoto, N, Kosako, Y, Tano, T (1991) Acidobacterium capsulatum gen. nov., sp. nov.; an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22: 1–7
Kuske, CR, Ticknot, OL, Miller, ME, Dunbar, JM, Davis, JA, Barns, SM, Belnap, J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and interspaces in an arid grassland. Appl Environ Microbiol 68: 1854–1863
Kumar, SK, Tamura, IB, Jakobsen, IB, Nei, M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244–1245
Muyzer, G, Hottentrager, S, Teske, A, Wawer, C (1996) Denaturing gradient electrophoresis of PCR-amplified 16S rDNA: a new molecular approach to analyse the genetic diversity of mixed microbial communities. In: Akkermans, ADL, van Elsas, JD, de Bruijn, FJ (Eds.) Molecular Microbial Ecology Manual. Kluwer Academic Publishers, The Netherlands, pp 1–23(3.4.4)
Muyzer, G, de Waal, EC, Uitterlinden, AG (1993) Profiling of complex microbial populations by denaturing gradient electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695–700
Muyzer, G, Teske, A, Wirsen, CO, Jannasch, HW (1995) Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165–172
Nagy, M, Pérez, A, Garcia-Pichel, F (2005) The prokaryotic diversity of biological soil crusts in the Sonoran desert (Organ Pipe Cactus National Monument, AZ). FEMS Microbiol Ecol 54: 233–245
Nakatsua, CH, Torsvik, V, Øvreås, L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64: 1382–1388
Nogales, B, Moore, ER, Llobet-Brossa, E, Rossello-Mora, R, Amann, R, Timmis, KN (2001) Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67: 1874–1884
Nübel, U, Garcia-Pichel, F, Muyzer, G (1997) PCR primers to amplify 16S rRNA genes from cyanobacteria. Appl Environ Microbiol 63: 3327–3332
Nübel, U, Garcia-Pichel, F, Kühl, M, Muyzer, G (1999) Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotinoids of oxygenic phototrophs in microbial mats. Appl Environ Microbiol 65: 422–430
Nubel, U, Garcia-Pichel, F, Clavero, E, Muyzer, G (2000) Matching molecular diversity and ecophysiology of benthic cyanobacteria and diatoms in communities along a salinity gradient. Environ Microbiol 2: 217–226
Purkhold, U, Wagner, M, Timmermann, G, Pommerening–Roser, A, Koops, HP (2003) 16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. Int J Syst Evol Microbiol 53: 1485–1494
Rothrock, MJ, Garcia-Pichel, F (2005) Microbial diversity of benthic mats along a tidal desiccation gradient. Environ Microbiol 7: 593–601
Shannon, CE, Weaver, W (1949) The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL
Smith, SM, Abed, RMM, Garcia-Pichel, F (2004) Biological soil crusts of sand dunes in Cape Cod National Seashore, Massachusetts, USA. Microbial Ecol 28: 200–208
Stackebrandt, E, Goebel, BM (1994) Taxanomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846–849
Thompson, JD, Higgins, DG, Gibson, TJ (1994) CLUSTAL W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680
von Wintzingerode, F, Selent, B, Hegemann, W, Gobel, UB (1999) Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl Environ Microbiol 65: 283–286
Wade, BD, Garcia-Pichel, F (2003) Evaluation of DNA extraction methods for molecular analyses of microbial communities in modern calcareous microbialites. Geomicrobiol J 20: 549–561
Yeager, CM, Kornosky, JL, Housman, DC, Grote, EE, Belnap, J, Kuske, CR (2004) Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Appl Environ Microbiol 70: 973–983
Zhang, H, Sekiguchi, Y, Hanada, S, Hugenholtz, P, Kim, H, Kamagata, Y, Nakamura, K (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53: 1155–1163